By the end of that century, however, San Francisco had become a polluted metropolis, with a culture that was described by various commentators as "primitive," "paranoid," and "medieval." The age seemed to have been characterized by greed, lack of proper medical care, and environmental crises, causing Leonard McCoy to consider it a miracle the citizens were able to survive into the 21st century. (Star Trek IV: The Voyage Home)

The city's social ills became even more pronounced by the 2020s. Massive unemployment and homelessness caused unrest in the streets. The government responded by instituting the system of Sanctuary Districts, requiring vagrants to live in segregated ghettos patrolled by law enforcement. Ostensibly, the Sanctuary Districts served only as temporary shelters until jobs could be found. In reality, they became a way to keep the segment of the population deemed "undesirable" out of the public eye.

The filmmakers of Star Trek proceeded from the notion that a cataclysm took place in San Francisco during the mid-21st century and was responsible for the loss of multiple buildings, requiring major reconstruction. (Cinefex, No. 118, pp. 60 & 64)

In 2368, archaeologists digging beneath the Presidio uncovered several artifacts from the late 19th century. Among several mundane artifacts was the severed head of Lieutenant CommanderData, which had been undisturbed for nearly five hundred years. It was learned that Data and several members of the USS Enterprise-D's crew had traveled back through time to late nineteenth century San Francisco in an effort to prevent the Devidians from draining the neural energy of Humans and disguising it as a cholera epidemic. While there, they met the noted humorist and prolific author Samuel Clemens. (TNG: "Time's Arrow")

In an alternate reality of 2372 visited by Harry Kim, parts of San Francisco were pedestrianized and served by public transports. In this reality, Kim lived in an apartment near a coffee shop called Cosimo's. Since the establishment's owner, Cosimo, was actually an alien whose time-streams Kim's shuttle intersected, it is unknown if the restaurant actually existed in the prime reality. (VOY: "Non Sequitur")

More shots of San Francisco were planned to appear in The Motion Picture than were ultimately completed for the film. A storyboard from the movie, depicting one of these unused shots, shows a walkway with a building on one side and a row of trees on the other, backgrounded by a skyline featuring multiple high-rises. (Star Trek: The Magazine Volume 2, Issue 8, p. 25)

Outdoor scenes featuring the Presidio were filmed at the Tillman Water Reclamation Plant and Gardens in Van Nuys, supplemented by a matte painting. 19th century San Francisco was actually a redress of the "Western" Universal Studios backlot set. Different sections of the same backlot were used for some of the street scenes in the 24th century as well. (citation needed • edit)

Star Trek IV: The Voyage Home was the only Star Trek movie or television production filmed substantially in San Francisco itself. When Leonard Nimoy and Harve Bennett relayed to Nicholas Meyer the story of that film prior to its making, Meyer's first reaction was to ask if San Francisco had to be the movie's main 20th-century setting, he having already made a film in which time-travelers end up in that city. Meyer wondered aloud about whether the former Enterprise crew couldn't go somewhere else "for a change," suggesting Paris as an alternative city. Nimoy and Bennett promptly replied that the San Francisco setting had to be used. "Ostensibly this had something to do with the fact of Starfleet Headquarters being based there," recalled Meyer, "but may more likely have been related to the fact that filming in San Francisco would be cheaper than attempting it in Paris." (The View from the Bridge - Memories of Star Trek and a Life in Hollywood)

For the film Star Trek, three or four different versions of 23rd-century San Francisco were developed in concept CGI illustrations. Stated Roger Guyett, "There would be no reason there still couldn't be current buildings around." (Star Trek - The Art of the Film, p. 51) Director J.J. Abrams intended to introduce the city with a static camera. "I wanted to do an establishing shot that was part of a scene," Abrams pointed out. "So you see... 'Look, there's future San Francisco.'" (audio commentary, xxx) The production shot aerial plates and scenic reference in the city, which Industrial Light & Magic significantly modified, adding towering buildings supposedly constructed to replace those lost in a mid-21st century cataclysm. As well as adding such futuristic and monothlithic structures, some fairly common reference sites were also used, such as the Transamerica Pyramid and the Golden Gate Bridge. The reuse of these locations helped maintain continuity with earlier Star Trek films. Views of the city predominantly consisted of three-dimensional structures layered through levels of haze, creating parallax effects. Footage set in the grounds of Starfleet Academy required the filmmakers to digitally expand the city from another angle. Associate Visual Effects Supervisor Eddie Pasquarello explained, "Some of our aerial shots of San Francisco began with a real plate; but by the time we were done, it was pretty much all 3D digimatte." (Cinefex, No. 118, pp. 60 & 64)

Various filming locations were used for the depictions of San Francisco in Star Trek Into Darkness. Industrial Light & Magic Senior Visual Effects Supervisor Roger Guyett recollected, "We used parts of the CAA building in Los Angeles as San Francisco. We modified them a lot, but the style of architecture allowed us to establish a lot of in-camera shots. This time we filmed Starfleet exteriors at the Getty Center in the Santa Monica Mountains, and we used Crystal Cathedral in Garden Grove as subsections of Starfleet." The filmmakers decided that, in San Francisco, buildings newer than the Golden Gate Bridge dwarfed the Transamerica Pyramid. After Roger Guyett shot visual effects plates and aerial reference footage in downtown San Francisco, Tiburon and Los Angeles, ILM developed environment extensions. "We started with the very tall and elongated city buildings that were featured briefly in the previous movie," explained ILM Art Director Yanick Dusseault. "In this movie, we were moving between buildings in 80 or 90 shots, so we had to get more intimate with the design. We spent a lot of time coming up with designs that fit Star Trek and the current city. San Francisco is the perfect location for capturing the Star Trek feel – it's very bright and airy, and fit the optimistic aesthetic." The ILM environments team created a model of futuristic San Francisco featuring sixty high-resolution buildings and then dressed in tiers of lower-resolution architecture. The high-resolution constructs could be exchanged and rotated to produce new configurations. (Cinefex, No. 134, pp. 72 & 74)

According to the Star Trek: Star Charts (p. 32), San Francisco was the capital of the North American continent.

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